simple scripts, in development, to be run after the merge with HAVANA
added new biotypes found by doing grep '^\#\=GF TP' /path/to/Rfam.seed | sort -u
Changes applied to add Gene.source and Transcript.source. PLEASE NOTE: This change is not backwards-copatible with old versions of the Core API. Older versions did not use transcript.source
Import APPRIS labels from CNIO eg. and write labels into transcript_attrib table
http://appris.bioinfo.cnio.es/download/data/gencodeM3/appris_data.principal.ForEnsembl.txt
Change to WGA2GenesDirect.pm and BaseGeneBuild.pm
For WGA2GenesDirect.pm pass in undef instead of empty string when creating the QUERY_DB database adaptor.
For BaseGeneBuild.pm, in the case of a non-standard dba being passed into get_dbadaptor it previously searched
for some information about the adapator requires, e.g. matching on 'compara' or 'functgen'. But if none of
these cases were matched it would just continue on without assigning anything. Put in an else in this case
which is just a throw
Change to BaseGeneBuild.pm
Update the text on the throw to point out that undef should be passed in for a
standard adaptor
Change to BaseGeneBuild.pm
Now with spelling
Change to TranscriptUtils.pm and WGA2GenesDirect.pm
In TranscriptUtils.pm, in the replace_stops_with_introns function there was the assumption that any transcript
passed in will have at least one internal stop. This is not always the case as WGA2GenesDirect.pm uses this
function to check all transcripts. Now a flag can be passed in, that allows multiple stops to be processed.
For the moment this flag is experimental, so if you're using it you should check the results. The function
will now no longer throw on transcripts that have no internal stops.

In addition I changed WGA2GenesDirect.pm to do a check on the peptide sequence of a transcript to see if there
are any internal stops present. This way the code should never call replace_stops_with_introns unless there is
a reason to begin with.
transcript_attrib.value now prints a brief description as well as the date
Changed TranscriptUtils.pm
Set  >= 1 in previous commit, should have been  > 1
Merge branch 'master' of https://github.com/Ensembl/ensembl-analysis
Only look at INSDC synonyms
splicing_event table has been removed from the schema (e76)
Changed TranscriptUtils.pm and WGA2GenesDirect.pm
Changed the logic in TranscriptUtils for the replace_stops sub. The logic now states that if the edited
translation is longer than the original, then throw. If the edited translation is shorter than the max
allowed removals, then throw. If the max_stops parameter is not defined and the number of stops removed
is greater than one, then throw. Otherwise it's okay.

For WGA2GenesDirect.pm I have set the max allowed removals to 10, however this might change in future.
Change WGA2GenesDirect.pm
Put in a max stop count of 10 when calling replace_stops, meant to be in previous commit
but value had been removed for testing purposes
Added support for HTA array
removed restrictive $ end of line match from header test, this can go in the regex config if required
Updated IIDREGEXP for AFFY_ST to support new HTA array
UpdFixed probe name test, now handles 0 as probe name
Merge wrapper use *_exclude and *_include